The purpose of this work is to develop methods for fractionating eukaryotic DNA so that specific fragments can be isolated in pure form. The method is generally applicable, but is particularly appropriate for non-transcribed regulatory and structural DNA sequences which cannot be purified by hybridization techniques. The essence of our approach is to integrate together fractionation methods which discriminate on the basis of base composition and sequence with the standard procedures of restriction enzyme digestion and gel electrophoretic size fractionation. The new methods rely on base composition- or sequence-dependent ligand binding, and include two-phase chromatographic and countercurrent distribution procedures having high capacity. In addition, gel electrophoresis methods which discriminate by base composition among equal sized DNA fragments will be developed. We also will develop rapid methods for screening DNA fragments on a gel electrophoretogram for ability to bind to a specific protein, and for assaying a large number of protein fractions for ability to bind specifically to a particular DNA. Initial applications of the methods will include localizing repeated DNA sequences on chromosomes, and a survey of the tissue-dependence of the reiteration frequency of particular sequences.